Different distributions of homologous chromosomes in adult human Sertoli cells and in lymphocytes signify nuclear differentiation

In Vitro and In Vivo Models for Drug Transport Across the Blood-Testis Barrier

The blood-testis barrier (BTB) is a selectively permeable membrane barrier formed by adjacent Sertoli cells (SCs) in the seminiferous tubules of the testes that develops intercellular junctional complexes to protect developing germ cells from external pressures. However, due to this inherent defense mechanism, the seminiferous tubule lumen can act as a pharmacological sanctuary site for latent viruses (e.g., Ebola, Zika) and cancers (e.g., leukemia). Therefore, it is critical to identify and evaluate BTB carrier-mediated drug delivery pathways to successfully treat these viruses and cancers. Many drugs are unable to effectively cross cell membranes without assistance from carrier proteins like transporters because they are large, polar, and often carry a charge at physiologic pH. SCs express transporters that selectively permit endogenous compounds, such as carnitine or nucleosides, across the BTB to support normal physiologic activity, although reproductive toxicants can also use these pathways, thereby circumventing the BTB. Certain xenobiotics, including select cancer therapeutics, antivirals, contraceptives, and environmental toxicants, are known to accumulate within the male genital tract and cause testicular toxicity; however, the transport pathways by which these compounds circumvent the BTB are largely unknown. Consequently, there is a need to identify the clinically relevant BTB transport pathways in in vitro and in vivo BTB models that recapitulate human pharmacokinetics and pharmacodynamics for these xenobiotics. This review summarizes the various in vitro and in vivo models of the BTB reported in the literature and highlights the strengths and weaknesses of certain models for drug disposition studies. SIGNIFICANCE STATEMENT: Drug disposition to the testes is influenced by the physical, physiological, and immunological components of the blood-testis barrier (BTB). But many compounds are known to cross the BTB by transporters, resulting in pharmacological and/or toxicological effects in the testes. Therefore, models that assess drug transport across the human BTB must adequately account for these confounding factors. This review identifies and discusses the benefits and limitations of various in vitro and in vivo BTB models for preclinical drug disposition studies.

Mitotic Antipairing of Homologous Chromosomes

Chromosome organization is highly dynamic and plays an essential role during cell function. It was recently found that pairs of the homologous chromosomes are continuously separated at mitosis and display a haploid (1n) chromosome set, or "antipairing," organization in human cells. Here, we provide an introduction to the current knowledge of homologous antipairing in humans and its implications in human disease.

The arrangement of Brachypodium distachyon chromosomes in interphase nuclei

The spatial organization of chromatin within the interphase nucleus and the interactions between chromosome territories (CTs) are essential for various biological processes, such as DNA replication, transcription, and repair. However, detailed data about the CT arrangement in monocotyledonous plants are scarce. In this study, chromosome painting was used to analyse the distribution and associations of individual chromosomes in the 3-D preserved nuclei of Brachypodium distachyon root cells in order to determine the factors that may have an impact on the homologous CT arrangement. It was shown that the frequency of CT association is linked to the steric constraints imposed by the limited space within the nucleus and may depend on chromosome size and morphology as well as on the nuclear shape. Furthermore, in order to assess whether the distribution of interphase chromosomes is random or is subject to certain patterns, a comparison between the experimental data and the results of a computer simulation (ChroTeMo), which was based on a fully probabilistic distribution of the CTs, was performed. This comparison revealed that homologous chromosome arm CTs associate more often than if they were randomly arranged inside the interphase nucleus.

Interphase chromatin organisation in Arabidopsis nuclei: constraints versus randomness

The spatial chromatin organisation and molecular interactions within and between chromatin domains and chromosome territories (CTs) are essential for fundamental processes such as replication, transcription and DNA repair via homologous recombination. To analyse the distribution and interaction of whole CTs, centromeres, (sub)telomeres and ~100-kb interstitial chromatin segments in endopolyploid nuclei, specific FISH probes from Arabidopsis thaliana were applied to 2-64C differentiated leaf nuclei. Whereas CTs occupy a distinct and defined volume of the nucleus and do not obviously intermingle with each other in 2-64C nuclei, ~100-kb sister chromatin segments within these CTs become more non-cohesive with increasing endopolyploidy. Centromeres, preferentially located at the nuclear periphery, may show ring- or half-moon like shapes in 2C and 4C nuclei. Sister centromeres tend to associate up to the 8C level. From 16C nuclei on, they become progressively separated. The higher the polyploidy level gets, the more separate chromatids are present. Due to sister chromatid separation in highly endopolyploid nuclei, the centromeric histone variant CENH3, the 180-bp centromeric repeats and pericentromeric heterochromatin form distinct subdomains at adjacent but not intermingling positions. The (sub)telomeres are frequently associated with each other and with the nucleolus and less often with centromeres. The extent of chromatid separation and of chromatin decondensation at subtelomeric chromatin segments varies between chromosome arms. A mainly random distribution and similar shapes of CTs even at higher ploidy levels indicate that in general no substantial CT reorganisation occurs during endopolyploidisation. Non-cohesive sister chromatid regions at chromosome arms and at the (peri)centromere are accompanied by a less dense chromatin conformation in highly endopolyploid nuclei. We discuss the possible function of this conformation in comparison to transcriptionally active regions at insect polytene chromosomes.

Similar rye A and B chromosome organization in meristematic and differentiated interphase nuclei

Supernumerary (B) chromosomes of rye are not required for plant development and exhibit a reduced transcription activity. These special features inspired us to analyse whether there are differences between A and B chromatin organization in interphase nuclei. Applying fluorescence in situ hybridization, we found that both rye A and B chromosomes added to hexaploid wheat showed in meristematic nuclei a string-like shape and a clear Rabl orientation. In 4C differentiated leaf nuclei, a more relaxed chromatin structure, round-shaped chromosome territories and a less pronounced Rabl configuration were found. Also, the observed random association of homologues in 2C and 4C nuclei indicated in general a similar behaviour of A and B chromosomes. Whereas in differentiated 4C nuclei A sister centromeres are separated, B sister centromeres align in nearly all nuclei. In short, despite the different transcription activity of A and B chromosomes, both types of chromosomes exhibit a similar organization in meristematic and differentiated interphase nuclei. But the deletion of a B chromosome segment responsible for non-disjunction during gametogenesis induces released sister centromeres also in some interphase nuclei of somatic tissue. Hence, the control of rye B chromosome non-disjunction is also active in sporophytic cells.

Distance between homologous chromosomes results from chromosome positioning constraints

The organization of chromosomes is important for various biological processes and is involved in the formation of rearrangements often observed in cancer. In mammals, chromosomes are organized in territories that are radially positioned in the nucleus. However, it remains unclear whether chromosomes are organized relative to each other. Here, we examine the nuclear arrangement of 10 chromosomes in human epithelial cancer cells by three-dimensional FISH analysis. We show that their radial position correlates with the ratio of their gene density to chromosome size. We also observe that inter-homologue distances are generally larger than inter-heterologue distances. Using numerical simulations taking radial position constraints into account, we demonstrate that, for some chromosomes, radial position is enough to justify the inter-homologue distance, whereas for others additional constraints are involved. Among these constraints, we propose that nucleolar organizer regions participate in the internal positioning of the acrocentric chromosome HSA21, possibly through interactions with nucleoli. Maintaining distance between homologous chromosomes in human cells could participate in regulating genome stability and gene expression, both mechanisms that are key players in tumorigenesis.

Chromatin dynamics

The expression patterns of many protein-coding genes are orchestrated in response to exogenous stimuli, as well as cell-type-specific developmental programs. In recent years, researchers have shown that dynamic chromatin movements and interactions in the nucleus play a crucial role in gene regulation. In this review, we highlight our current understanding of the organization of chromatin in the interphase nucleus and the impact of chromatin dynamics on gene expression. We also discuss the current state of knowledge with regard to the localization of active and inactive genes within the three-dimensional nuclear space. Furthermore, we address recent findings that demonstrate the movements of chromosomal regions and genomic loci in association with changes in transcriptional activity. Finally, we discuss the role of intra- and interchromosomal interactions in the control of coregulated genes.

Random homologous pairing and incomplete sister chromatid alignment are common in angiosperm interphase nuclei

The chromosome arrangement in interphase nuclei is of growing interest, e.g., the spatial vicinity of homologous sequences is decisive for efficient repair of DNA damage by homologous recombination, and close alignment of sister chromatids is considered as a prerequisite for their bipolar orientation and subsequent segregation during nuclear division. To study the degree of homologous pairing and of sister chromatid alignment in plants, we applied fluorescent in situ hybridisation with specific bacterial artificial chromosome inserts to interphase nuclei. Previously we found in Arabidopsis thaliana and in A. lyrata positional homologous pairing at random, and, except for centromere regions, sister chromatids were frequently not aligned. To test whether these features are typical for higher plants or depend on genome size, chromosome organisation and/or phylogenetic affiliation, we investigated distinct individual loci in other species. The positional pairing of these loci was mainly random. The highest frequency of sister alignment (in >93% of homologues) was found for centromeres, some rDNA and a few other high copy loci. Apparently, somatic homologous pairing is not a typical feature of angiosperms, and sister chromatid aligment is not obligatory along chromosome arms. Thus, the high frequency of chromatid exchanges at homologous positions after mutagen treatment needs another explanation than regular somatic pairing of homologues (possibly an active search of damaged sites for homology). For sister chromatid exchanges a continuous sister chromatid alignment is not required. For correct segregation, permanent alignment of sister centromeres is sufficient.

Common themes and cell type specific variations of higher order chromatin arrangements in the mouse

Background

Similarities as well as differences in higher order chromatin arrangements of human cell types were previously reported. For an evolutionary comparison, we now studied the arrangements of chromosome territories and centromere regions in six mouse cell types (lymphocytes, embryonic stem cells, macrophages, fibroblasts, myoblasts and myotubes) with fluorescence in situ hybridization and confocal laser scanning microscopy. Both species evolved pronounced differences in karyotypes after their last common ancestors lived about 87 million years ago and thus seem particularly suited to elucidate common and cell type specific themes of higher order chromatin arrangements in mammals.

Results

All mouse cell types showed non-random correlations of radial chromosome territory positions with gene density as well as with chromosome size. The distribution of chromosome territories and pericentromeric heterochromatin changed during differentiation, leading to distinct cell type specific distribution patterns. We exclude a strict dependence of these differences on nuclear shape. Positional differences in mouse cell nuclei were less pronounced compared to human cell nuclei in agreement with smaller differences in chromosome size and gene density. Notably, the position of chromosome territories relative to each other was very variable.

Conclusion

Chromosome territory arrangements according to chromosome size and gene density provide common, evolutionary conserved themes in both, human and mouse cell types. Our findings are incompatible with a previously reported model of parental genome separation.

[Topographical organisation of the chromatin in human interphase nuclei: architecture meets function]

There are an estimated number of 30,000 genes in the human genome, accounting for as few as 5% of the whole DNA content. Determining the exact role of the vast majority of untranscribed DNA is a major goal for upcoming years. Among various evolutionary constrains which could explain the presence of such a quantity of so-called "junk DNA", one hypothesis is the necessary controlled topographical arrangement of the genome during interphase, leading to a non-random, reproducible position of chromosomal regions inside the nucleus. This hypothesis relies on recent progresses in imaging technologies such as fluorescence confocal microscopy, allowing for the first time the identification of each chromosome-specific chromatin during interphase. This review focuses on the past years advances leading to the actual model of chromosome territories in the interphase nucleus.

Chromosome territory arrangement and homologous pairing in nuclei of Arabidopsis thaliana are predominantly random except for NOR-bearing chromosomes

Differential painting of all five chromosome pairs of Arabidopsis thaliana revealed for the first time the interphase chromosome arrangement in a euploid plant. Side-by-side arrangement of heterologous chromosome territories and homologous association of chromosomes 1, 3 and 5 (on average in 35-50% of nuclei) are in accordance with the random frequency predicted by computer simulations. Only the nucleolus organizing region (NOR)-bearing chromosome 2 and 4 homologs associate more often than randomly, since NORs mostly attach to a single nucleolus. Somatic pairing of homologous approximately 100 kb segments occurs less frequently than homolog association, not significantly more often than expected at random and not simultaneously along the homologs. Thus, chromosome arrangement in Arabidopsis differs from that in Drosophila (characterized by somatic pairing of homologs), in spite of similar genome size, sequence organization and chromosome number. Nevertheless, in up to 31.5% of investigated Arabidopsis nuclei allelic sequences may share positions close enough for homologous recombination.

Chromosomes of the budding yeast Saccharomyces cerevisiae

The mitotic chromosomes of the baker's yeast, Saccharomyces cerevisiae, cannot be visualized by standard cytological methods. Only the study of meiotic bivalents and the synaptonemal complex and the visualization of chromosome-sized DNA molecules on pulsed-field gels have provided some insight into chromosome structure and behavior. More recently, advanced techniques such as in situ hybridization, the illumination of chromosomal loci by GFP-tagged DNA-binding proteins, and immunostaining of chromosomal proteins have promoted our knowledge about yeast chromosomes. These novel cytological approaches in combination with the yeast's advanced biochemistry and genetics have produced a great wealth of information on the interplay between molecular and cytological processes and have strengthened the role of yeast as a leading cell biological model organism. Recent cytological studies have revealed much about the chromosomal organization in interphase nuclei and have contributed significantly to our current understanding of chromosome condensation, sister chromatid cohesion, and centromere orientation in mitosis. Moreover, important details about the biochemistry and ultrastructure of meiotic pairing and recombination have been revealed by combined cytological and molecular approaches. This article covers several aspects of yeast chromosome structure, including their organization within interphase nuclei and their behavior during mitosis and meiosis.

A model for interphase chromosomes and evaluation of radiation-induced aberrations

We have developed a theoretical model for evaluating radiation-induced chromosomal exchanges by explicitly taking into account interphase (G(0)/G(1)) chromosome structure, nuclear organization of chromosomes, the production of double-strand breaks (DSBs), and the subsequent rejoinings in a faithful or unfaithful manner. Each of the 46 chromosomes for human lymphocytes (40 chromosomes for mouse lymphocytes) is modeled as a random polymer inside a spherical volume. The chromosome spheres are packed randomly inside a spherical nucleus with an allowed overlap controlled by a parameter Omega. The rejoining of DSBs is determined by a Monte Carlo procedure using a Gaussian proximity function with an interaction range parameter sigma. Values of Omega and sigma have been found which yield calculated results of interchromosomal aberration frequencies that agree with a wide range of experimental data. Our preferred solution is one with an interaction range of 0.5 microm coupled with a relatively small overlap parameter of 0.675 microm, which more or less confirms previous estimates. We have used our model with these parameter values and with resolution or detectability limits to calculate yields of translocations and dicentrics for human lymphocytes exposed to low-LET radiation that agree with experiments in the dose range 0.09 to 4 Gy. Five different experimental data sets have been compared with the theoretical results. Essentially all of the experimental data fall between theoretical curves corresponding to resolution limits of 1 Mbp and 20 Mbp, which may reflect the fact that different investigators use different limits for sensitivity or detectability. Translocation yields for mouse lymphocytes have also been calculated and are in good agreement with experimental data from 1 cGy to 10 cGy. There is also good agreement with recent data on complex aberrations. Our model is expected to be applicable to both low- and high-LET radiation, and we include a sample prediction of the yield of interchromosomal rejoining in the dose range 0.22 Gy to 2 Gy of 1000 MeV/nucleon iron particles. This dose range corresponds to average particle traversals per nucleus ranging from 1.0 to 9.12.

Chromosome territories, nuclear architecture and gene regulation in mammalian cells

The expression of genes is regulated at many levels. Perhaps the area in which least is known is how nuclear organization influences gene expression. Studies of higher-order chromatin arrangements and their dynamic interactions with other nuclear components have been boosted by recent technical advances. The emerging view is that chromosomes are compartmentalized into discrete territories. The location of a gene within a chromosome territory seems to influence its access to the machinery responsible for specific nuclear functions, such as transcription and splicing. This view is consistent with a topological model for gene regulation.

Size-dependent positioning of human chromosomes in interphase nuclei

By using a fluorescence in situ hybridization technique we revealed that for nine different q-arm telomere markers the positioning of chromosomes in human G(1) interphase nuclei was chromosome size-dependent. The q-arm telomeres of large chromosomes are more peripherally located than telomeres on small chromosomes. This highly organized arrangement of chromatin within the human nucleus was discovered by determining the x and y coordinates of the hybridization sites and calculating the root-mean-square radial distance to the nuclear centers in human fibroblasts. We demonstrate here that global organization within the G(1) interphase nucleus is affected by one of the most fundamental physical quantities-chromosome size or mass-and propose two biophysical models, a volume exclusion model and a mitotic preset model, to explain our finding.

Higher levels of organization in the interphase nucleus of cycling and differentiated cells

The review examines the structured organization of interphase nuclei using a range of examples from the plants, animals, and fungi. Nuclear organization is shown to be an important phenomenon in cell differentiation and development. The review commences by examining nuclei in dividing cells and shows that the organization patterns can be dynamic within the time frame of the cell cycle. When cells stop dividing, derived differentiated cells often show quite different nuclear organizations. The developmental fate of nuclei is divided into three categories. (i) The first includes nuclei that undergo one of several forms of polyploidy and can themselves change in structure during the course of development. Possible function roles of polyploidy is given. (ii) The second is nuclear reorganization without polyploidy, where nuclei reorganize their structure to form novel arrangements of proteins and chromosomes. (iii) The third is nuclear disintegration linked to programmed cell death. The role of the nucleus in this process is described. The review demonstrates that recent methods to probe nuclei for nucleic acids and proteins, as well as to examine their intranuclear distribution in vivo, has revealed much about nuclear structure. It is clear that nuclear organization can influence or be influenced by cell activity and development. However, the full functional role of many of the observed phenomena has still to be fully realized.

Genome organization in the human sperm nucleus studied by FISH and confocal microscopy

The sperm nucleus has a unique chromatin structure where the DNA is highly condensed and associated with specific proteins, the protamines. It is a nondividing cell which is also transcriptionally inactive. After fusion with an oocyte, the sperm nucleus undergoes decondensation and, in the same time, starts replication and transcription. It has been suggested that somatic chromosomes during interphase are organized in territories which display a cell type and cell cycle specific distribution. The purpose of this work was to investigate whether chromosomes would also have a specific distribution in the sperm nucleus, which could be related to its inactive state, and have implications on the early stages of fertilization. In the present study, centromeric and telomeric sequences were detected by fluorescent techniques performed on human decondensed spermatozoa. Chromosome painting probes were used to detect the chromosome X and chromosome 13 on interphase sperm nuclei. The fluorescent signals were captured in 3D with a confocal microscope. For each of these chromatin structures, the volume, position, and distribution of the signals were analyzed in samples of 30 nuclei with the help of image analysis software. The centromeres appeared grouped in several foci that were randomly distributed within the sperm nucleus. The telomeres gave an approximately haploid number of small signals, evenly distributed throughout the nucleus. The chromosomes X and 13 occupied 4.7% and 3. 7% of the total nuclear volume, respectively. Interestingly, the X chromosome territory showed a preferential position in the anterior half of the volume of the nucleus, whereas chromosome 13 had a random position. This work shows a particular distribution of chromosome territories in the human sperm nucleus that could be related to mechanisms implicated in its specific functions. The analysis of more chromosomes and chromosomal structures, including the Y chromosome, would help to understand the structure of the human sperm chromatin, and its fundamental and clinical implications.

Chromosomes exhibit preferential positioning in nuclei of quiescent human cells

The relative spatial positioning of chromosomes 7, 8, 16, X and Y was examined in nuclei of quiescent (noncycling) diploid and triploid human fibroblasts using fluorescence in situ hybridization (FISH) with chromosome-specific DNA probes and digital imaging. In quiescent diploid cells, interhomolog distances and chromosome homolog position maps revealed a nonrandom, preferential topology for chromosomes 7, 8 and 16, whereas chromosome X approximated a more random distribution. Variations in the orientation of nuclei on the culture substratum tended to hinder detection of an ordered chromosome topology at interphase by biasing homolog position maps towards random distributions. Using two chromosome X homologs as reference points in triploid cells (karyotype = 69, XXY), the intranuclear location of chromosome Y was found to be predictable within remarkably narrow spatial limits. Dual-FISH with various combinations of chromosome-specific DNA probes and contrasting fluorochromes was used to identify adjacent chromosomes in mitotic rosettes and test whether they are similarly positioned in interphase nuclei. From among the combinations tested, chromosomes 8 and 11 were found to be closely apposed in most mitotic rosettes and interphase nuclei. Overall, results suggest the existence of an ordered interphase chromosome topology in quiescent human cells in which at least some chromosome homologs exhibit a preferred relative intranuclear location that may correspond to the observed spatial order of chromosomes in rosettes of mitotic cells.